312cb15592bc68cc8d16269dc98feaae *DESCRIPTION
21284418f400c991e1307b2251ff2bcc *NAMESPACE
2b25b67fc49f606cb7e8b1f0e9c1b161 *R/BioTIP-package.R
3d6308dc6b26eeaa39ad103e1c6ee9d1 *R/BioTIP_update_06232025.R
6057716cfd4e3920dcdbf106b795d020 *R/data.R
92f755396e22304d675558e4d60844c1 *README.md
cf74989e201549c5a0fc3bd08a15ac7d *build/vignette.rds
d50d2715c35ac54025595620f8cb4617 *data/GSE6136_cli.RData
86fe0cfb62e24e2df1502c89b5397931 *data/GSE6136_matrix.RData
79ad48ff275d45c4caa8e403f15ac0be *data/ILEF.RData
6b1c16b3fe2bb5ccb981985bcae3147f *data/cod.RData
c3f28e8a38f39a0ed5b568e92bb3482a *data/gencode.RData
67798ef176494381a350558e8752c62a *data/intron.RData
076f7bea3ac8286aac106308aeed7ef9 *data/membersL.RData
335d625ebd4109073aa87158b659f167 *data/subcounts.optimize_80per.RData
5d619caf96104d066d39ccb9412e1003 *examples/BioTIP.wrap_09092022.R
33f8b7fa8197871a19a686523f5ecf12 *examples/code/EB_Zhao2019/1_GSE130146_EB_process.R
48a7128c9cf588483a9edae3eb5058cb *examples/code/EB_Zhao2019/2_GSE130146_runBioTP.R
bba47dc4084925a95f6181e50b7ce9a9 *examples/code/EB_Zhao2019/3_plotHVG_trajectory.R
0f0a188cb7ee26c64e32faa24b1ac5f2 *examples/code/EB_Zhao2019/4_plotIc.randomGene.R
ed02b9218e23a81b903be0376986e83f *examples/code/EB_Zhao2019/readme.txt
ff72377c7e63bce6917ba7d8a80c584e *examples/code/Stability_score.R
7cbe6a2d4a047cbc0dd8f66dc7fdc0b2 *examples/code/barplot_Jarcard_DNB.Ic.BioTIP.QuanTC_6dbs.R
2163759ae8080527e91f4cb6a1a058db *examples/code/gastrulationE8.25_Ibarra-Soria2018/1_E-MTAB-6153_normalized_count.R
b68933393e5eb9c9efeb57d92f1c837c *examples/code/gastrulationE8.25_Ibarra-Soria2018/2_BioTIP_E-MTAB-6153_E8.25.2018.R
8eca6bb0582bc280adf6101e78cb615b *examples/code/gastrulationE8.25_Ibarra-Soria2018/3_plotHVG_trajectory.R
4ea4269aa8ba91c40bf6e9ac26cc1544 *examples/code/gastrulationE8.25_Ibarra-Soria2018/4_plotIc.randomGene.R
b8b787692b1b327d0cd3350d920881ff *examples/code/gastrulationE8.25_Ibarra-Soria2018/readme.txt
4ee3b7cad59990804ca2ade5008f9322 *examples/code/gastrulationE8.25_Pijuan-Sala2019/2.1_E8.25_mesoderm_add.clusterIDs.R
63f27136133f7f12435e255395ae0556 *examples/code/gastrulationE8.25_Pijuan-Sala2019/2.2_E8.25_mesoderm_runBioTP_different.clustering.R
a9b7f526236fdbaca02ea0b4156d057a *examples/code/gastrulationE8.25_Pijuan-Sala2019/2.3_E8.25_mesoderm_quantify_robustness.R
691898d098c8c6a1f1d57976c9d16d8e *examples/code/gastrulationE8.25_Pijuan-Sala2019/3_E8.25_mesoderm_runBioTIP_stability_1360cell.R
db1bfd4589c71558eefbd0a3081360e4 *examples/code/gastrulationE8.25_Pijuan-Sala2019/4_evaluation.CTS_using2018data.R
7330e9006baf154d8b598ed60b401d19 *examples/code/gastrulationE8.25_Pijuan-Sala2019/5_plotIc.randomGene.R
574afb807b44204f848173b69af4d9a1 *examples/code/gastrulationE8.25_Pijuan-Sala2019/BioTIP.tune.parameter.R
ff72377c7e63bce6917ba7d8a80c584e *examples/code/gastrulationE8.25_Pijuan-Sala2019/Stability_score.R
9983ab4aa3f562be80a58ba326895c5b *examples/code/gastrulationE8.25_Pijuan-Sala2019/myplotIc.R
0b4eecd214cf0bad8696bdf32b1a99be *examples/code/gastrulationE8.25_Pijuan-Sala2019/readme.txt
7271a2a329f7868f46fc7a5a1eb56dba *examples/code/hESC_Bargaje2017/1.1_data_matrix_Cluster_CMpath.R
a5584c2059404a6cf3b2ca28e4fb2ae6 *examples/code/hESC_Bargaje2017/1.2_data_matrix_timepoint.R
8c8ea11fa0e2019f4ef73b6799c53d9b *examples/code/hESC_Bargaje2017/2.1_hESC_Bargaje2017_add.clusterIDs.R
ca8e86567f1c61f20e7f78306c1735a1 *examples/code/hESC_Bargaje2017/2.2_hESC_Bargaje2017_runBioTP_different.clustering.R
30d4524686e279321d8749816eb171fd *examples/code/hESC_Bargaje2017/2.3_hESC_Bargaje2017_quantify_robustness.R
520e2239a2db4f1b101410cbd88b672b *examples/code/hESC_Bargaje2017/3_hESC_Bargaje2017_runBioTP_stability.R
b9cc70b0b058cfef39eef5541de23ab2 *examples/code/hESC_Bargaje2017/4_plotIc.randomGene.R
b8b787692b1b327d0cd3350d920881ff *examples/code/hESC_Bargaje2017/readme.txt
d80ded0c4119c2e46a17327a514210a6 *examples/code/lung_Treutlein2014/1_FPKM_preprocess.R
6664c63c34feac88dee00a70a2b22e10 *examples/code/lung_Treutlein2014/2_Treutlein2014_runBioTP.R
ddfeb748c53fea38ecaae0baa703409c *examples/code/lung_Treutlein2014/3_BioTIP_GSE52583_feature.selection.plot.R
be7bb4037e75d82d5689abe7a3233a8a *examples/code/lung_Treutlein2014/4_plotIc.randomGene.R
b8b787692b1b327d0cd3350d920881ff *examples/code/lung_Treutlein2014/readme.txt
9983ab4aa3f562be80a58ba326895c5b *examples/code/myplotIc.R
5699968d5cc06a249ce6c3a7169e5e6f *examples/code/simulated_EMT/0_export_data.m
7889ec8e22e2d31d5fc27249dc7a5957 *examples/code/simulated_EMT/1_QuanTC.data.load_SC3.inputs.R
250595206246bf136d279aed7df176f4 *examples/code/simulated_EMT/2_Add.cluster_BioTIP.run.R
034002492a14ed8270bfc50d6af20ed7 *examples/code/simulated_EMT/3_Plot.R
cddef9b74a2f9fe005105f5c78c2a07d *examples/code/simulated_EMT/4_plotIc.randomGene.R
b8b787692b1b327d0cd3350d920881ff *examples/code/simulated_EMT/readme.txt
4bfe1dccb8a2bdacb7a6135846215b51 *inst/doc/BioTIP.R
6713d33211b2a2b49758fbf021e74bee *inst/doc/BioTIP.Rmd
0dd93027fdb718605fc8f237b9c28d48 *inst/doc/BioTIP.html
aa1e6e53f694519d974e48055640567f *man/BioTIP-package.Rd
9f6d64b795a6b6b351a51364f43a1a46 *man/GSE6136_cli.Rd
2ec2252a2bf6f6f2b7397a48771d38bb *man/GSE6136_matrix.Rd
57a41ced8561cab6324200c90c504f1c *man/ILEF.Rd
44869c29462757e75ffec5b78f366702 *man/avg.cor.shrink.Rd
9b1fbb6f45db66069ead4b657504fca6 *man/cod.Rd
ee59af557114b536e0fcc6081c9fb670 *man/cor.shrink.Rd
8950784dd0ea63708ddbb6d50e99c316 *man/gencode.Rd
a7b8f3cf00fdc2e9a112f25ede94eb9f *man/getBiotypes.Rd
e7483ac2be6ac49542855bd34caa1323 *man/getCTS.Rd
4e649d17e215986719e6cb7cd68d35b6 *man/getCluster_methods.Rd
67458d3c5a34b13eff82722ef8d7477c *man/getIc.Rd
84fe8e4f196f6c89d3fe9b6615917214 *man/getIc.new.Rd
97b0d3f107bcab06f0161b07f8c8faf6 *man/getMCI.Rd
681bbec464d9d4017677fe11d37bc34c *man/getMCI_inner.Rd
5417f4f7f2e46ab2c66fcff5ceb5797f *man/getMaxMCImember.Rd
8c3d674fd2e9ab033d6bb20dc7ce9a57 *man/getMaxStats.Rd
770a03961899ffb9fcdcf464e8903831 *man/getNetwork.Rd
30b41832338ab5f0c93bfddc13bc2286 *man/getReadthrough.Rd
b1b4fa3b531348949349f9f5bbee9b2f *man/intron.Rd
e38c0520fae76fea79ee7cfdaa2f217d *man/optimize.sd_selection.Rd
a42df3f80c05da4592ea638c00767b0d *man/plotBar_MCI.Rd
1a038c5a101a3b64953c7158de1b1144 *man/plotIc.Rd
66d166988bf5cd7b3c6fc9114e900ae3 *man/plotMaxMCI.Rd
eff27c714dccb84c1fd4b33789b5f878 *man/plot_Ic_Simulation.Rd
6ab6c5ed7b379ce81e72b44a52dde2af *man/plot_MCI_Simulation.Rd
26cc77d0abac73a317d850c924557578 *man/plot_SS_Simulation.Rd
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581b66511bd036c549227e8ca771517d *man/simulationMCI.Rd
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57cd10205a8c5895fe859f526317a3bc *man/simulation_Ic_sample.Rd
6713d33211b2a2b49758fbf021e74bee *vignettes/BioTIP.Rmd
7df9cef98b3502635d6a24a1efa2bd52 *vignettes/CTS_Id.jpg
7306de4002d539bbb9c131383a4b0e59 *vignettes/DNB_Sim_M.jpg
d96c4d14e12c9481ee44739abf579db9 *vignettes/Fig1_scRNARNAseq_pipeline_2021_xy.jpg
3ccd1902d61d59639d217629a08eb4ca *vignettes/Fig2.jpg
a9e1513a0a2ccc442ee29dd2e64af4b3 *vignettes/FigS1_BioTIP_pipeline_detailed_v7.jpg
4ab808ecb890236a6b4de99d38fd317c *vignettes/Fig_Table1_xy.jpg
6aa415a1c6bf20986db4a1873cc704f3 *vignettes/cell_info.tsv
9ebda484649959b967b3da02abf8b72f *vignettes/chr21.JPG
3733ffbab552a1e99cd54b19317d2697 *vignettes/delta.jpg
f631c190d39b70644b72375468e93dff *vignettes/subway_map.jpg
f901a4e1a993e414ebe8fe3ddf9f0031 *vignettes/subway_map.pdf
